Only the rear window comes out of the Trektop. The new Trektop NX will have all three windows removable, and it has the sunrider feature, iirc. Plus it comes with a better header and door surrounds than the old one.
They are due out soon, not sure on the release date as those things are subject to change. No, I don't have one, I have a friend who has the original Trektop on his LJ, and he loves it, but he doesn't use his Jeep for much except a weekend cruise. I understand that they are a bit more trouble to install/remove than a top with a frame, but most who have them say it's maybe 5 extra minutes. The biggest challenge will be if you want to carry it with you, expecting weather... They are bulky.
Yea because of what infernogirl said and when I got it it took for ever to get on and off. And when it's off you really can't store it in you jeep so if your topless and it starts to rain your out of luck